ArticleProceedings of the National Academy of Sciences of the United States of America2009
Finding of residues crucial for supersecondary structure formation.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- The 3D Invariant Positioning for Protein Molecules / Molecular Complexes with Matching Subunits.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Amino acid distribution rules predict protein fold: protein grammar for beta-strand sandwich-like structures.Biomolecules · 2015Article
- Contribution to the prediction of the fold code: application to immunoglobulin and flavodoxin cases.PloS one · 2015Article
- Identification of an ideal-like fingerprint for a protein fold using overlapped conserved residues based approach.Scientific reports · 2014Article
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2 authors.
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Abstract
This work evaluates the hypothesis that proteins with an identical supersecondary structure (SSS) share a unique set of residues--SSS-determining residues--even though they may belong to different protein families and have very low sequence similarities. This hypothesis was tested on two groups of sandwich-like proteins (SPs). Proteins in each group have an identical SSS, but their sequence similarity is below the "twilight zone." To find the SSS-determining residues specific to each group, a unique structure-based algorithm of multiple sequences alignment was developed. The units of alignment are individual strands and loops rather than whole sequences. The algorithm is based on the alignment of residues that form hydrogen bonds between corresponding strands. Structure-based alignment revealed that 30-35% of the positions in the sequences in each group of proteins are "conserved positions" occupied either by hydrophobic-only or hydrophilic-only residues. Moreover, each group of SPs is characterized by a unique set of SSS-determining residues found at the conserved positions. The set of SSS-determining residues has very high sensitivity and specificity for identifying proteins with a corresponding SSS: It is an "amino acid tag" that brands a sequence as having a particular SSS. Thus, the sets of SSS-determining residues can be used to classify proteins and to predict the SSS of a query amino acid sequence.
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